Package list python-pauvre / upstream/0.2.1
New upstream version 0.2.1 Andreas Tille 1 year, 5 months ago
10 changed file(s) with 40 addition(s) and 84 deletion(s). Raw diff Collapse all Expand all
00 Metadata-Version: 1.2
11 Name: pauvre
2 Version: 0.1924
2 Version: 0.2.1
33 Summary: Tools for plotting Oxford Nanopore and other long-read data.
44 Home-page: https://github.com/conchoecia/pauvre
55 Author: Darrin Schultz
66 Author-email: dts@ucsc.edu
7 License: GPLv3
7 License: UNKNOWN
88 Description:
99 'pauvre' is a package for plotting Oxford Nanopore and other long read data.
1010 The name means 'poor' in French, a play on words to the oft-used 'pore' prefix
1616 Classifier: Development Status :: 2 - Pre-Alpha
1717 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
1818 Classifier: Programming Language :: Python :: 3
19 Classifier: Programming Language :: Python :: 3.5
19 Classifier: Programming Language :: Python :: 3.6
20 Classifier: Programming Language :: Python :: 3.7
2021 Classifier: Operating System :: POSIX :: Linux
2122 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
2223 Classifier: Intended Audience :: Science/Research
23 Requires: python (>3.0)
24 Provides: pauvre
2524 Requires-Python: >=3
2222 parsimonius rotation to display the synteny of all the input
2323 genomes with the fewest crossings-over. Input is one `.gff` file
2424 per circular genome and one directory of gene alignments.
25
26 ## Updates:
27 - 20200215 - v0.1.924 - Made some minor updates to work with python 3.7 and the latest version of pandas,
28 - 20171130 - v0.1.86 - some changes by @wdecoster to integrate `pauvre` into [nanoplot](https://github.com/wdecoster/NanoPlot),
29 as well as some formatting changes that *may* make `pauvre` work better with python2.7. Adding Travis-CI functionality.
30 - 20171025 - v0.1.83 - added some changes to make marginplot interface
31 with @wdecoster's [nanoPlot](https://github.com/wdecoster/NanoPlot)
32 package, and made `pauvre stats` only output data tables for
33 filtered reads. `pauvre stats` also now has the `--filt_maxlen`,
34 `--filt_maxqual`, `--filt_minlen`, and `--filt_minqual` options.
35 - 20171018 - v0.1.8 - you can now filter reads and adjust the plotting viewing window.
36 [See below for a demonstration.](#filter-reads-and-adjust-viewing-window) I added the following options:
37
38 ```
39 --filt_maxlen FILT_MAXLEN
40 This sets the max read length filter reads.
41 --filt_maxqual FILT_MAXQUAL
42 This sets the max mean read quality to filter reads.
43 --filt_minlen FILT_MINLEN
44 This sets the min read length to filter reads.
45 --filt_minqual FILT_MINQUAL
46 This sets the min mean read quality to filter reads.
47 --plot_maxlen PLOT_MAXLEN
48 Sets the maximum viewing area in the length dimension.
49 --plot_maxqual PLOT_MAXQUAL
50 Sets the maximum viewing area in the quality
51 dimension.
52 --plot_minlen PLOT_MINLEN
53 Sets the minimum viewing area in the length dimension.
54 --plot_minqual PLOT_MINQUAL
55 Sets the minimum viewing area in the quality
56 dimension.
57 ```
58 - 20171014 - uploading information on `pauvre redwood` and `pauvre synteny` usage.
59 - 20171012 - made `pauvre stats` more consistently produce useful histograms.
60 `pauvre stats` now also calculates some statistics for different size ranges.
61 - 20170529 - added automatic scaling to the input fastq file. It
62 scales to show the highest read quality and the top 99th percentile
63 of reads by length.
6425
6526 # Requirements
6627
377377 min_plot_qual, max_plot_qual, min_plot_length, max_plot_length),
378378 file=stderr)
379379 # Print image(s)
380 if kwargs["BASENAME"] is None and not kwargs["path"] is None:
381 file_base = kwargs["BASENAME"]
382 elif kwargs["BASENAME"] is None:
380 if kwargs["BASENAME"] is None:
383381 file_base = opath.splitext(opath.basename(kwargs["fastq"]))[0]
384382 else:
385383 file_base = kwargs["BASENAME"]
44 def update_rcParams():
55 # This mpl style is from the UCSC BME163 class.
66 rcParams.update({
7 'font.size' : 8.0 ,
8 'font.sans-serif' : 'Arial' ,
9 'xtick.major.size' : 2 ,
10 'xtick.major.width' : 0.75 ,
11 'xtick.labelsize' : 8.0 ,
12 'xtick.direction' : 'out' ,
13 'ytick.major.size' : 2 ,
14 'ytick.major.width' : 0.75 ,
15 'ytick.labelsize' : 8.0 ,
16 'ytick.direction' : 'out' ,
17 'xtick.major.pad' : 2 ,
18 'xtick.minor.pad' : 2 ,
19 'ytick.major.pad' : 2 ,
20 'ytick.minor.pad' : 2 ,
21 'savefig.dpi' : 601 ,
22 'axes.linewidth' : 0.75 ,
23 'text.usetex' : False ,
24 'text.latex.unicode' : False })
7 'font.size' : 8.0 ,
8 'font.sans-serif' : 'Arial' ,
9 'xtick.major.size' : 2 ,
10 'xtick.major.width' : 0.75 ,
11 'xtick.labelsize' : 8.0 ,
12 'xtick.direction' : 'out' ,
13 'ytick.major.size' : 2 ,
14 'ytick.major.width' : 0.75 ,
15 'ytick.labelsize' : 8.0 ,
16 'ytick.direction' : 'out' ,
17 'xtick.major.pad' : 2 ,
18 'xtick.minor.pad' : 2 ,
19 'ytick.major.pad' : 2 ,
20 'ytick.minor.pad' : 2 ,
21 'savefig.dpi' : 601 ,
22 'axes.linewidth' : 0.75 ,
23 'text.usetex' : False ,
24 "image.composite_image": False ,
25 "pdf.fonttype" : 42,
26 "ps.fonttype" : 42 })
27
702702 end = time.time()
703703 print(end - start)
704704 # Print image(s)
705 ifargs.BASENAME is None:
705 if args.BASENAME is None:
706706 file_base = "redwood"
707707 else:
708708 file_base = args.BASENAME
00 # -*- coding: utf-8 -*-
11
2 __version__ = "0.1924"
2 __version__ = "0.2.1"
3
00 Metadata-Version: 1.2
11 Name: pauvre
2 Version: 0.1924
2 Version: 0.2.1
33 Summary: Tools for plotting Oxford Nanopore and other long-read data.
44 Home-page: https://github.com/conchoecia/pauvre
55 Author: Darrin Schultz
66 Author-email: dts@ucsc.edu
7 License: GPLv3
7 License: UNKNOWN
88 Description:
99 'pauvre' is a package for plotting Oxford Nanopore and other long read data.
1010 The name means 'poor' in French, a play on words to the oft-used 'pore' prefix
1616 Classifier: Development Status :: 2 - Pre-Alpha
1717 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
1818 Classifier: Programming Language :: Python :: 3
19 Classifier: Programming Language :: Python :: 3.5
19 Classifier: Programming Language :: Python :: 3.6
20 Classifier: Programming Language :: Python :: 3.7
2021 Classifier: Operating System :: POSIX :: Linux
2122 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
2223 Classifier: Intended Audience :: Science/Research
23 Requires: python (>3.0)
24 Provides: pauvre
2524 Requires-Python: >=3
22 pandas>=0.20.1
33 numpy>=1.12.1
44 scipy
5 sklearn
5 scikit-learn
00 #!/usr/bin/env python3
11 # -*- coding: utf-8 -*-
22
3 # pauvre
3 # pauvre
44 # Copyright (c) 2016-2020 Darrin T. Schultz.
55 #
66 # This file is part of pauvre.
2727
2828 version_py = os.path.join(os.path.dirname(__file__), 'pauvre', 'version.py')
2929 version = open(version_py).read().strip().split('=')[-1].replace('"', '').strip()
30 print(version)
3130
3231
3332 setup(name='pauvre',
34 requires=['python (>3.0)'],
3533 version=version,
3634 description='Tools for plotting Oxford Nanopore and other long-read data.',
3735 long_description="""
4139 python 2. You can visit the gitub page for more detailed information here:
4240 https://github.com/conchoecia/pauvre
4341 """,
44
4542 url='https://github.com/conchoecia/pauvre',
4643 author='Darrin Schultz',
4744 author_email='dts@ucsc.edu',
4946 'Development Status :: 2 - Pre-Alpha',
5047 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
5148 'Programming Language :: Python :: 3',
52 'Programming Language :: Python :: 3.5',
49 'Programming Language :: Python :: 3.6',
50 'Programming Language :: Python :: 3.7',
5351 'Operating System :: POSIX :: Linux',
5452 'Topic :: Scientific/Engineering :: Bio-Informatics',
55 'Intended Audience :: Science/Research'
53 'Intended Audience :: Science/Research',
5654 ],
57 license='GPLv3',
58 provides=['pauvre'],
59 packages=find_packages() + ['scripts'],
55 packages=find_packages(),
6056 python_requires='>=3',
6157 install_requires=[
6258 "matplotlib >= 2.0.2",
6460 "pandas >= 0.20.1",
6561 "numpy >= 1.12.1",
6662 "scipy",
67 "sklearn"
63 "scikit-learn",
6864 ],
6965 entry_points={
7066 'console_scripts': ['pauvre=pauvre.pauvre_main:main'],